Saccharomyces cerevisiae Reference Assembly Panel Database (ScRAPdb)
Saccharomyces cerevisiae Reference Assembly Panel Database (ScRAPdb)
A searchable table of the S. cerevisiae pangenome ORFs defined in Peter et al. (2018) Nature (LINK) is provided below. The listed core/accessory classification and origin assignment are based on the original study. Click on the PanORF ID to find out the detailed presence/absence pattern of the corresponding pangenome ORF in both ScRAPdb and the 1002ScGP strain collections (which were recalculated by ScRAPdb).
| PanORF ID | SGD systematic Name | SGD standard name | Alias | Description | Type | Origin assignment | Mostly likely origin species | NCBI megablast hit |
|---|---|---|---|---|---|---|---|---|
| 4193-YHL001W | YHL001W | RPL14B | eL14|ribosomal 60S subunit protein L14B|L14e|L14B | Ribosomal 60S subunit protein L14B; homologous to mammalian ribosomal protein L14, no bacterial homolog; RPL14B has a paralog, RPL14A, that arose from the whole genome duplication; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 4194-YHL002W_NumOfGenes_2 | YHL002W | HSE1 | ESCRT-0 subunit protein HSE1 | Subunit of the endosomal Vps27p-Hse1p complex; complex is required for sorting of ubiquitinated membrane proteins into intralumenal vesicles prior to vacuolar degradation, as well as for recycling of Golgi proteins and formation of lumenal membranes | Core | NA | NA | NA |
| 4195-YHL003C | YHL003C | LAG1 | sphingosine N-acyltransferase LAG1 | Ceramide synthase component; involved in synthesis of ceramide from C26(acyl)-coenzyme A and dihydrosphingosine or phytosphingosine, functionally equivalent to Lac1p; forms ER foci upon DNA replication stress; homolog of human CERS2, a tumor metastasis suppressor gene whose silencing enhances invasion/metastasis of prostate cancer cells; LAG1 has a paralog, LAC1, that arose from the whole genome duplication | Core | NA | NA | NA |
| 4196-YHL004W | YHL004W | MRP4 | mitochondrial 37S ribosomal protein MRP4 | Mitochondrial ribosomal protein of the small subunit | Core | NA | NA | NA |
| 4197-YHL005C | YHL005C | NA | NA | Putative protein of unknown function; conserved among S. cerevisiae strains; YHL005C is not an essential gene | Core | NA | NA | NA |
| 4198-YHL006C | YHL006C | SHU1 | NA | Component of Shu complex (aka PCSS complex); Shu complex also includes Psy3, Csm2, Shu2, and promotes error-free DNA repair, mediates inhibition of Srs2p function; essential for promoting the establishment of homolog bias during meiotic homologous recombination; promotes both crossover (CO) and non-crossover (NCO) pathways of meiotic recombination and formation of Rad51p filaments | Core | NA | NA | NA |
| 4199-YHL006W-A | YHL006W-A | NA | NA | Dubious open reading frame; unlikely to encode a functional protein, based on available experimental and comparative sequence data; overlaps ORF STE20/YHL007C | Accessory | Ancestral | NA | NA |
| 4200-YHL007C | YHL007C | STE20 | mitogen-activated protein kinase kinase kinase kinase STE20 | Cdc42p-activated signal transducing kinase; involved in pheromone response, pseudohyphal/invasive growth, vacuole inheritance, down-regulation of sterol uptake; GBB motif binds Ste4p; member of the PAK (p21-activated kinase) family | Accessory | Ancestral | NA | NA |
| 4201-YHL008C | YHL008C | NA | NA | Putative protein of unknown function; may be involved in the uptake of chloride ions; does not appear to be involved in monocarboxylic acid transport; green fluorescent protein (GFP)-fusion protein localizes to the vacuole | Accessory | Ancestral | NA | NA |
| 4202-YHL009C | YHL009C | YAP3 | NA | Basic leucine zipper (bZIP) transcription factor | Accessory | Ancestral | NA | NA |
| 4203-YHL010C | YHL010C | ETP1 | BRP2 | Protein of unknown function required for growth on ethanol; contains a zinc finger region and has homology to human BRAP2, which is a cytoplasmic protein that binds nuclear localization sequences | Accessory | Ancestral | NA | NA |
| 4204-YHL011C | YHL011C | PRS3 | ribose phosphate diphosphokinase subunit PRS3 | 5-phospho-ribosyl-1(alpha)-pyrophosphate synthetase; synthesizes PRPP, which is required for nucleotide, histidine, and tryptophan biosynthesis; one of five related enzymes, which are active as heteromultimeric complexes | Accessory | Ancestral | NA | NA |
| 4205-YHL012W | YHL012W | NA | UTP--glucose-1-phosphate uridylyltransferase | Putative UTP glucose-1-phosphate uridylyltransferase; YHL012W has a paralog, UGP1, that arose from the whole genome duplication | Accessory | Ancestral | NA | NA |
| 4206-YHL013C | YHL013C | OTU2 | NA | Protein of unknown function; may interact with ribosomes, based on co-purification experiments; member of the ovarian tumor-like (OTU) superfamily of predicted cysteine proteases; shows cytoplasmic localization; protein abundance increases in response to DNA replication stress | Accessory | Ancestral | NA | NA |
| 4207-YHL014C | YHL014C | YLF2 | YLF1 | Protein of unknown function; has weak similarity to E. coli GTP-binding protein gtp1; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies | Accessory | Ancestral | NA | NA |